4PYU: Ubiquitin-like protein 5

The conserved ubiquitin-like protein hub1 plays a critical role in splicing in human cells. Determined by X-ray diffraction at 2.0 Å resolution. Released 16 Jul 2014.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 12
Atoms: 4,741
Mol. weight: 65.75 kDa
Released: 16 Jul 2014

Explore 4PYU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4PYU contains 32 α-helices and 42 β-strands across 12 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains A and B: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-7	7	1
β-strand	13-19	7	1
β-strand	23	1	2
α-helix	24-35	12
α-helix	39-41	3
β-strand	42-46	5	1
β-strand	49-50	2	1
β-strand	56	1	2
α-helix	62-63	2
β-strand	67-72	6	1

Chain C: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-12	10
α-helix	15-17	3

Chains D, L and T: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-13	11
α-helix	15-17	3

Chain G: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-8	8	5
β-strand	13-19	7	5
β-strand	23	1	6
α-helix	24-35	12
α-helix	39-41	3
β-strand	42-46	5	5
β-strand	49-50	2	5
α-helix	51-52	2
β-strand	56	1	6
α-helix	58-60	3
α-helix	66	1
β-strand	67-72	6	5

Chains H and P: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-13	11

Chain K: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-8	8	7
β-strand	13-19	7	7
β-strand	23	1	8
α-helix	24-35	12
β-strand	42-46	5	7
β-strand	49-50	2	7
α-helix	51-52	2
β-strand	56	1	8
α-helix	58-60	3
β-strand	67-72	6	7

Chains O and S: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-8	8	9
β-strand	13-19	7	9
β-strand	23	1	10
α-helix	24-35	12
α-helix	39-41	3
β-strand	42-46	5	9
β-strand	49-50	2	9
α-helix	51-52	2
β-strand	56	1	10
α-helix	58-60	3
β-strand	67-72	6	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-like protein 5	A, B, G, K, O, S	protein	76	Homo sapiens	Q9BZL1 (AlphaFold model)
U4/U6.U5 tri-snRNP-associated protein 1	C, D, H, L, P, T	protein	19	Homo sapiens	O43290 (AlphaFold model)

Sequence of entity 1 (A, B, G, K, O, S), FASTA

>4PYU_1 Ubiquitin-like protein 5 (chains A, B, G, K, O, S)
GSHMIEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKKWYTIFKDHVSL
GDYEIHDGMNLELYYQ

Sequence of entity 2 (C, D, H, L, P, T), FASTA

>4PYU_2 U4/U6.U5 tri-snRNP-associated protein 1 (chains C, D, H, L, P, T)
SLSIEETNKLRAKLGLKPL

Primary citation

The conserved ubiquitin-like protein Hub1 plays a critical role in splicing in human cells. Ammon, T., Mishra, S.K., Kowalska, K. et al. J Mol Cell Biol (2014) 6:312-323. DOI 10.1093/jmcb/mju026 · PubMed

Other PDB entries of the same protein (UniProt Q9BZL1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8H6K 2.7 Å, Cryo-EM structure of human exon-defined spliceosome in the mature B state.
8Q7N 3.1 Å, cryo-EM structure of the human spliceosomal B complex protomer (tri-snRNP core region)
9R3D 3.12 Å, Cryo-EM structure of the human pre-Bact-OTS complex (whole map)
6AHD 3.8 Å, The Cryo-EM Structure of Human Pre-catalytic Spliceosome (B complex) at 3.8 angstrom…
7ABF 3.9 Å, Human pre-Bact-1 spliceosome core structure
7AAV 4.2 Å, Human pre-Bact-2 spliceosome core structure
8QO9 5.29 Å, Cryo-EM structure of a human spliceosomal B complex protomer
7ABG 7.8 Å, Human pre-Bact-1 spliceosome
7ABI 8.0 Å, Human pre-Bact-2 spliceosome
9R8V 8.5 Å, Cryo-EM structure of the human pre-Bact-OTS complex (whole map)
1P0R Solution Structure of UBL5 a human Ubiquitin-Like Protein

Browse structure collections

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